DNA profiling and applications (9.3.3) | OCR A-Level Biology Notes

OCR Specification focus:
‘Describe principles of DNA profiling and its uses in forensic analysis and assessing genetic disease risk.’

DNA profiling identifies individuals by analysing variations in their DNA. It underpins modern forensic science, paternity testing, and medical genetics, offering powerful diagnostic and investigative tools.

Principles of DNA Profiling

The Basis of DNA Variation

Every individual (except identical twins) has a unique DNA sequence. Most human DNA is identical, but non-coding regions, particularly short tandem repeats (STRs), vary greatly between individuals. STRs are short sequences of bases repeated in tandem at specific loci.

Short Tandem Repeat (STR): A short sequence of DNA bases (2–13 nucleotides) repeated in series at the same position (locus) in the genome.

The number of repeats at each locus differs between individuals, forming a unique genetic fingerprint when several loci are analysed.

Stages in DNA Profiling

1. Sample Collection and DNA Extraction

DNA is extracted from biological materials such as blood, saliva, hair roots, or skin cells. The sample is purified to remove contaminants that could inhibit further analysis.

2. DNA Amplification

Polymerase Chain Reaction (PCR) is used to amplify specific STR regions. This ensures sufficient DNA is available for analysis even from trace samples.

3. DNA Fragment Separation by Electrophoresis

DNA fragments are separated according to size using gel electrophoresis or capillary electrophoresis. Shorter fragments migrate faster through the gel or capillary.

Diagram of gel electrophoresis used in DNA fingerprinting. DNA samples are loaded into wells; an electric field separates fragments so smaller fragments migrate further, producing bands that can be compared between individuals. This clean schematic mirrors how forensic gels are interpreted in practice. Source.

4. Detection and Analysis

The separated fragments are visualised using fluorescent markers or radioactive labels. The pattern of STRs forms the DNA profile of the individual.

Capillary electrophoresis electropherogram showing STR peaks (signal intensity vs fragment length). Peaks correspond to alleles at loci, and their positions are used to assign genotypes and build a DNA profile for comparison. This output format underpins modern forensic and kinship analyses. Source.

5. Comparison

The resulting DNA profile is compared with reference samples. Matching profiles indicate the same origin, while differing profiles exclude a match.

Techniques Used in DNA Profiling

Restriction Fragment Length Polymorphism (RFLP)

Historically, RFLP analysis used restriction enzymes to cut DNA at specific sequences. Differences in fragment lengths were visualised by electrophoresis and Southern blotting. Although accurate, RFLP required large samples and was time-consuming, so it has been replaced by modern PCR-based methods.

STR Profiling

Modern profiling focuses on STR analysis because:

STRs are highly polymorphic.
Only small DNA quantities are required.
PCR enables rapid and automated processing.
STR data are easily stored in databases such as the UK National DNA Database (NDNAD).

Interpretation of DNA Profiles

DNA profiles are interpreted by comparing multiple STR loci. The probability of two unrelated individuals sharing the same STR pattern is extremely low. Statistical analysis determines the match probability or random match probability — the likelihood that a coincidental match occurs.

Match Probability: The likelihood that two DNA profiles from unrelated individuals appear identical by chance.

Combining data from multiple loci exponentially reduces the probability of a false match, increasing the reliability of identification.

Applications of DNA Profiling

1. Forensic Analysis

DNA profiling revolutionised forensic science by allowing identification of suspects from minute biological traces. Common applications include:

Identifying suspects through comparison with DNA found at crime scenes.
Exonerating individuals wrongly accused or convicted.
Identifying victims of disasters, such as plane crashes or mass casualties.

Forensic laboratories maintain strict chain of custody and quality assurance protocols to prevent contamination and ensure admissibility in court.

2. Paternity and Family Testing

DNA profiling confirms biological relationships by comparing STR patterns between individuals. In paternity testing:

A child inherits one allele per STR locus from each parent.
Matching patterns between the alleged father and child confirm relatedness.

Allele: One of two or more alternative forms of a gene or DNA sequence found at a specific locus on a chromosome.

Family testing also assists in immigration cases and identifying remains through kinship analysis.

3. Assessing Genetic Disease Risk

DNA profiling extends to medical genetics by detecting inherited genetic variations linked to disease susceptibility.

Specific alleles or STR patterns near disease-associated genes can act as genetic markers.
Profiling can identify carriers of recessive disorders or individuals at risk of multifactorial diseases (e.g., cancer predispositions).

While DNA profiling itself does not diagnose diseases, it guides genetic counselling and preventive healthcare.

4. Conservation and Wildlife Biology

Profiling aids in identifying individuals and monitoring genetic diversity in endangered species. It also combats wildlife crime by tracing illegally traded animal products.

5. Historical and Archaeological Identification

Ancient DNA profiling has identified historical figures and human remains, aiding anthropological and genealogical research.

Reliability and Limitations

Reliability

Modern DNA profiling is highly accurate when protocols are followed. Analysing multiple STR loci minimises the risk of coincidental matches. DNA evidence is thus powerful in both criminal justice and genetic research.

Limitations

However, DNA profiling has limitations:

Contamination from other DNA sources can compromise results.
Partial or degraded samples may yield incomplete profiles.
Database errors or false inclusions can occur through poor interpretation.
Ethical concerns arise from storing genetic data and potential misuse of DNA databases.

Ethical and Legal Considerations

DNA profiling raises important ethical issues surrounding privacy, consent, and data retention. In the UK, legislation regulates:

Collection and storage of DNA samples by law enforcement.
Rights to remove DNA data after acquittal.
Appropriate use of genetic information in healthcare and insurance.

Balancing individual rights with public safety remains an ongoing debate in policy and law.

FAQ

STR loci are chosen because they are highly polymorphic and show independent inheritance. This means each locus contributes uniquely to an individual's genetic profile.

For forensic use, loci are:

Located on different chromosomes or far apart to avoid linkage.
Short in length (2–6 base pairs repeated) to survive DNA degradation.
Well characterised with known population allele frequencies.

Standardised STR sets, such as the UK’s NDNAD or the US CODIS system, ensure consistent profiling across laboratories.

Capillary electrophoresis is faster, more sensitive, and highly automated compared to traditional agarose gels.

It uses narrow glass capillaries filled with a polymer matrix and applies high voltage to separate DNA fragments based on size.
Key advantages include:

Digital, computer-based data output (electropherograms).
Reduced contamination risk due to closed systems.
Accurate sizing and detection through fluorescent labelling.

These features make it ideal for forensic and clinical applications requiring precision and reproducibility.

Each STR locus has multiple possible alleles with specific frequencies in a population. The probability of two unrelated individuals sharing a genotype at one locus is calculated using these allele frequencies.

The overall match probability is determined by multiplying probabilities from all independent loci (product rule).
For example:
If locus A = 1/10, locus B = 1/20, and locus C = 1/50, the combined probability = 1/10 × 1/20 × 1/50 = 1/10,000.

This shows that analysing more loci greatly increases identification confidence.

Degraded DNA may lose longer fragments, causing incomplete STR profiles. Forensic scientists use miniSTRs, which target shorter sequences, improving success with damaged samples.

In mixed samples, such as from multiple individuals, overlapping STR peaks appear. Analysts interpret these using statistical software and knowledge of allele frequencies to identify potential contributors.

Strict laboratory controls and replicate analyses help confirm results and reduce interpretation errors.

DNA databases raise concerns about privacy, consent, and potential misuse. While they aid crime detection, retaining personal genetic data can infringe individual rights.

Key ethical issues include:

Retaining profiles of innocent individuals or minors.
Potential discrimination based on genetic information.
Risk of unauthorised access or data leaks.

Balancing public safety with civil liberties remains a key policy debate in the governance of forensic databases.

Practice Questions

Question 1 (2 marks)
Explain why short tandem repeats (STRs) are used in DNA profiling rather than coding regions of DNA.

Mark Scheme:

1 mark for stating that STRs show high variability between individuals.
1 mark for stating that coding regions are highly conserved or similar between individuals.
(Allow alternative phrasing such as “STRs are polymorphic whereas coding sequences are mostly identical.”)

Question 2 (5 marks)
Describe the main stages involved in producing a DNA profile from a crime scene sample and explain how the resulting data can be used to identify a suspect.